masschroq file parameters associated to project

src/core/project.cpp

@@ -29,6 +29,7 @@
 
 Project::Project()
 {
+  msp_masschroqFileParametersSp = std::make_shared<MasschroqFileParameters>();
 }
 
 Project::~Project()
@@ -272,8 +273,8 @@ Project::startGrouping(WorkMonitorInterface *p_work_monitor)
   qDebug();
   for(IdentificationGroup *p_id_group : _identification_goup_list)
     {
-      p_id_group->startGrouping(
-        m_contaminantRemovalMode, m_groupingType, p_work_monitor);
+      p_id_group->startGrouping(m_contaminantRemovalMode, m_groupingType,
+                                p_work_monitor);
     }
   qDebug();
 }
@@ -301,14 +302,12 @@ Project::hasPtmExperiment() const
 void
 Project::getSameXicPeptideEvidenceList(
   std::vector<const PeptideEvidence *> &peptide_evidence_list,
-  const MsRun *p_msrun,
-  const PeptideXtp *p_peptide,
-  unsigned int charge) const
+  const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
 {
   for(const IdentificationGroup *p_ident_group : _identification_goup_list)
     {
-      p_ident_group->getSameXicPeptideEvidenceList(
-        peptide_evidence_list, p_msrun, p_peptide, charge);
+      p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
+                                                   p_msrun, p_peptide, charge);
     }
 }
 
@@ -544,3 +543,9 @@ Project::isTarget(PeptideEvidence *p_pe) const
     }
   return false;
 }
+
+const MasschroqFileParametersSp &
+Project::getMasschroqFileParametersSp() const
+{
+  return msp_masschroqFileParametersSp;
+}

src/core/project.h

@@ -208,8 +208,7 @@ class Project
    */
   void getSameXicPeptideEvidenceList(
     std::vector<const PeptideEvidence *> &peptide_evidence_list,
-    const MsRun *p_msrun,
-    const PeptideXtp *p_peptide,
+    const MsRun *p_msrun, const PeptideXtp *p_peptide,
     unsigned int charge) const;
 
 
@@ -239,6 +238,10 @@ class Project
    */
   bool isTarget(PeptideEvidence *p_pe) const;
 
+  /** @brief get MassChroQ parameters specific to this project
+   */
+  const MasschroqFileParametersSp &getMasschroqFileParametersSp() const;
+
   private:
   LabelingMethodSp _labeling_method_sp;
   ProjectMode _project_mode = ProjectMode::combined;
@@ -263,4 +266,5 @@ class Project
   MsRunStore _msrun_store;
   FastaFileStore _fasta_file_store;
   bool m_project_changed = false;
+  MasschroqFileParametersSp msp_masschroqFileParametersSp;
 };

src/gui/masschroq_run_dialog/masschroqfileparameters.h

@@ -36,6 +36,9 @@
 #include <pappsomspp/processing/filters/filtersuitestring.h>
 #include "../../core/msrun.h"
 
+class MasschroqFileParameters;
+typedef std::shared_ptr<MasschroqFileParameters> MasschroqFileParametersSp;
+
 struct MasschroqFileParameters
 {
   void save() const;
@@ -63,7 +66,7 @@ struct MasschroqFileParameters
 
   pappso::XicExtractMethod xic_extraction_method; // sum or max
 
-  std::vector<MsRunAlignmentGroupSp> alignment_groups;
-
   pappso::FilterSuiteStringSPtr msp_xicFilterSuiteString;
+
+  std::vector<MsRunAlignmentGroupSp> alignment_groups;
 };